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Sample GSM862485 Query DataSets for GSM862485
Status Public on Jun 07, 2012
Title PDCCETumor_FreshFrozen_CRC083X1A
Sample type RNA
 
Source name mouse derived colorectal explant tumor, colorectal primary, fresh frozen tissue
Organism Homo sapiens
Characteristics primary tumor site: colorectal
sample type: PDCCE tumor
metastatic tumor site: peritoneal
Treatment protocol N/A
Growth protocol Human tumors were resected at time of surgery and flash frozen in OCT (Optimal Cutting Temperature) on dry ice. To generate patient-derived colorectal explants (PDCCEs), the collected human tumor samples were washed with PBS and then minced into 2~3 mm cubes. The samples were then placed in an enzyme medium (RPMI media containing collagenase IV, hyaluronidase and deoxyribonuclease) and agitated at room temperature for 18-24h. After agitation, the cells were spun down, washed with PBS and passed through a cell strainer. To eliminate red blood cells, 2-3 ml of red blood cell lysis buffer were added to the cells and incubated at 37°C for 5 min. After washing with PBS, the cells were centrifuged at 2000 rpm for 15 min at room temperature, resuspended in serum free-RPMI Matrigel mixture (1:1 volume) and then injected into the flanks of 4-week-old female JAX NOD.CB17-PrkdcSCID-J mice under a Duke IACUC approved protocol.
Extracted molecule total RNA
Extraction protocol Human tumors were flash frozen in OCT at time of surgical resection. PDCCE tumors were harvested at the end of 3 weeks and flash frozen in OCT. For both human tumors and PDCCEs, an initial section was stained with Hematoxylin and Eosin for histological characterization of the tissue, and the sample was subsequently macrodissected to ensure > 80% tumor. Approximately 100 ug of tissue was macrodissected, and total RNA was isolated from the homogenized tissue using the RNAase Isolation Kit (Qiagen, Valencia, Ca). Additionally, PDCCEs were also fixed in formalin overnight or 3 days and paraffin embedded the following day. RNA from the FFPE tumor samples was then extracted using the High Pure RNA Paraffin Kit (Roche).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol The resulting biotin-labeled RNA samples were then hybridized with Affymetrix U133A 2.0 GeneChip arrays according to the manufacturer's instructions (Affymetrix, Santa Clara, CA).
Scan protocol GeneChips were scanned using the Gene Array Scanner (Affymetrix) following the manufacturer’s instructions (Affymetrix, Santa Clara, CA).
Data processing The data were analyzed using the R statistical platform with the Bioconductor affymetrix package.
 
Submission date Jan 17, 2012
Last update date Jun 07, 2012
Contact name David Hsu
Organization name Duke University
Department Medical Oncology
Street address 905 S. LaSalle St. Rm 3008
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platform ID GPL570
Series (1)
GSE35144 Molecular Evaluation of Patient-Derived Colorectal Cancer Explants as a Pre-clinical Mouse Model of Colorectal Cancer

Data table header descriptions
ID_REF
VALUE Log2 GC-RMA signal.

Data table
ID_REF VALUE
1007_s_at 12.09458781
1053_at 9.094216925
117_at 7.683156717
121_at 9.876851549
1255_g_at 4.43755039
1294_at 9.082132533
1316_at 7.585440115
1320_at 6.240300564
1405_i_at 7.585392221
1431_at 4.765215047
1438_at 9.609073749
1487_at 9.654688155
1494_f_at 7.304436885
1552256_a_at 10.93253024
1552257_a_at 9.869104932
1552258_at 6.752281323
1552261_at 6.730655034
1552263_at 8.859898637
1552264_a_at 9.102418106
1552266_at 5.455749867

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM862485.CEL.gz 5.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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